[gmx-users] Problem concerning topology

Heikki Käsnänen hkasnane at hytti.uku.fi
Fri May 28 08:53:07 CEST 2004

Dear gmx-users,

I've been trying to run simulations with G-protein coupled receptor and DPPC
-lipid bilayer. I've used gromacs-hole to generate the hole to the bilayer.
After merging the protein and bilayer with genbox I'm having some serious
problems to get the right topology file for grompp.

Grompp gives this error: Fatal error: Atoms in the .top are not numbered
consecutively from 1.

I've even tried to renumber my dppc.itp file to follow the atom numbering of the
protein.itp file. Although I think this isn't even mandatory. I'm using gromacs314.

My .top file is like this:

 ; molecules
#include "/home2/farop/hkasnane/gromacs/real/FF/FF/ffgmx.itp"
#include "/home2/farop/hkasnane/gromacs/real/FF/FF/lipid.itp"
#include "/home2/farop/hkasnane/gromacs/real/FF/FF/dppc.itp"
#include "/home2/farop/hkasnane/gromacs/real/FF/FF/protein.itp"

#ifdef FLEX_SPC
#include "flexspc.itp"
#include "spc.itp"

#include "/home2/farop/hkasnane/gromacs/real/FF/FF/dppc.itp"
#ifdef POSRES
#include "/home2/farop/hkasnane/gromacs/real/FF/FF/lipid_posre.itp"

[ system ]
; name

[ molecules ]
; name	number
DPPC    52
SOL     6874
Protein 1

Is there any ideas how to overcome this problem?

Best wishes,

Heikki Kasnanen
Department of pharmaceutical chemistry
University of Kuopio

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